I am doing a targeted amplicon NGS analysis on cholangiocarcinoma FFPE samples on proton sequencer on a run with 88% ISP loading. The XLS file provided, containing all the barcodes that went into analysis with the variantCaller (v220.127.116.11) software in IonServer has two different columns for reference and variant alleles that seem to differ in a portion of cases within the same row. For my example the differences were observed in 50/1743 variants. How should I treat these variants ? Keep one of the pair of values or reject them altogether ?